Figure 4.

Different scenarios for how two genes A and B may switch from non-overlapping to overlapping,
and vice versa. The solid boxes, empty boxes, and empty boxes with arrows are coding
exons, 5' UTRs, and 3' UTRs, respectively. Genes A and B are in red and blue, respectively.
Cases a-d denote same-strand overlapping genes, while cases e-h denote different-strand
overlapping genes. From a non-overlapping state to an overlapping state: (a) Extension
of the 3' UTR in gene A due to loss of the transcription stop signal results in extension
of gene A into gene B. Here the extension creates only a partial overlap, but a large
extension may cover the entire gene B. (b) Emergence of a new 3' UTR exon in gene
A results in the complete embedment of gene B within gene A. Unlike case (a), case
(b) requires the creation of a new exon, so that it is less likely to occur than case
(a). (c) Emergence of a new transcription start site extends the 5' UTR in gene B
to partially cover the 3' UTR of gene A. If the extension is long, it may entirely
cover gene A. (d) Emergence of a new 5' UTR exon in gene B upstream of gene A results
in the embedment of gene A completely inside gene B. (e) Extension of the 3' UTR in
gene A due to loss of the transcription stop signal results in extension of gene A
into gene B. Here the extension creates only a partial overlap, but a large extension
may cover the entire gene B. (f) Emergence of a new 3' UTR exon in gene A results
in the complete embedment of gene B inside gene A. (g) Extension of the 5' UTR of
gene A in the 5' direction creates a partial overlap of gene A with gene B. (h) Emergence
of a new 5' UTR exon in gene A results in the complete embedment of gene B inside
gene A. The opposite scenarios to the above would create a transition from the overlapping
state to a non-overlapping state of two neighboring genes.